svim

Identify structural variants in long-read DNA sequencing BAM files using SVIM

usage

nexus run --nf-workflow variant_calling_svim.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --reference_genome_fasta_file /path/to/file.fasta \
    --params_svim "--min_mapq 20 --min_sv_size 30 --insertion_sequences --read_names --zmws"

Note

Nextflow config files are available here. Use the config file that matches your installed nexus version (e.g. nexus_v0.2.0_nextflow_slurm.config).

parameters

parameter	description
--samples_tsv_file	TSV file with the following columns: ‘sample_id’, ‘bam_file’, ‘bam_bai_file’.
--output_dir	Directory to which output files will be copied.
--reference_genome_fasta_file	Reference genome FASTA file.
--params_svim	SVIM parameters (default: ‘“–min_mapq 20 –min_sv_size 30 –insertion_sequences –read_names –zmws”’). Note that the parameters need to be wrapped in quotes.